7X9L

Crystal structure of MutT-8-oxo-dGTP complex: Reaction for 4 hr using 10 mM Mn2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A6T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP288potassium sodium tartrate, sodium citrate, ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.1542.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.531α = 90
b = 56.106β = 90
c = 59.369γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102005-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11SPring-8BL38B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8232.3297.70.07119.85.31169811.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.890.247

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISFREE R-VALUE3A6T1.8232.321.391167056397.470.15380.15240.181114.27
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.9296
f_angle_d1.1651
f_chiral_restr0.0601
f_bond_d0.0061
f_plane_restr0.0051
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1055
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms54

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction